Metabolism is a fascinating natural production and distribution process. Metabolic systems can be represented as a layered network, where the input layer consists of all the nutrients in the environment (raw materials entering the production process in the cell), subsequently to be processed by a complex network of biochemical reactions (middle layer) and leading to a well-defined output pattern, optimizing, for example, cell growth. Mathematical frameworks exploiting this layered-network representation of metabolism allow the prediction of metabolic fluxes (the cell’s ‘material flow’) under diverse conditions. In combination with suitable minimal models, it is possible to identify fundamental design principles and understand the efficiency and robustness of metabolic systems. Here, we summarize some design principles of metabolic systems from the perspective of production logistics and explore, how these principles can serve as templates for the design of robust manufacturing systems.